The EpiTect ChIP PCR Array is
a panel of 96 primer assays for pathway or
disease-focused genes in a 96-well or 384-well
plate. These primer assays are designed and
optimized for the pathway-focused analysis of in
vivo protein-DNA interactions. The EpiTect ChIP
PCR array performs ChIP DNA analysis with
real-time PCR sensitivity and the multi-genomic
loci profiling capability of ChIP-on-chip.
Simply mix your ChIP DNA sample with the
appropriate RT² SYBR™ Green PCR master mix,
aliquot equal volumes into each well of the
array plate, and then run the real-time PCR
cycling program. Following real-time PCR,
analyze your data using the free, downloadable
Excel template.

Figure 1. Uniform Amplification Efficiency and Specific PCR Detection.
A panel of 96 ChIP-qPCR primers were randomly selected from the genome-wide
primer pool and analyzed for their performance. (A) All assays exhibit an
average amplification efficiency of 99% with a 104.5% confidence interval
between 102.5-105.2%. The uniformly high amplification efficiency ensures
accurate analysis of multiple genomic loci simultaneously using the ΔΔCt method.
(B) Each ChIP-qPCR primer assay is experimentally validated using
dissociation (melt) curve analysis and agarose gel verification. Each pair of
primers on EpiTect ChIP PCR Array produces a single specific product as
indicated by a single dissociation curve peak at a melting temperature (Tm)
greater than 75 ºC, and is further validated by agarose gel for single product
of predicted size.

ReproducibilityThe complete EpiTect ChIP PCR Array System demonstrates a high degree of reproducibility across technical replicates, production lots, real-time PCR instruments, and different end-users, ensuring reliable detection of differences in genomic DNA enrichment among biological samples.

Figure 2. Consistent Performance within the Same Plate or across Different
Plates. Sonicated chromatin from HeLa cells
(20 µg) was immunoprecipitated with 2 µg of
anti-H3ac antibody or control IgG for 2 hours
using the EpiTect ChIP One-Day Kit. ChIP DNA
samples were characterized in triplicates with
EpiTect ChIP qPCR primers specific for active
genes (GAPDH, RPL30, ALDOA), inactive genes
(MYOD1, SERPINA), repetitive sequence (SAT2,
SATa), and an ORF-free region (IGX1A) either
within the same array plate or among different
array plates in order to evaluate the intra- and
inter-plate consistency. The anti-H3ac antibody
enriched genomic DNA at active gene promoter
regions with a high signal-to-noise ratio and a
low co-efficiency of variation (less than
2.02%), irrespective of the type of assay (intra
or inter-plate).

Figure 3. Consistent Performance with Various Amount of DNA Samples,
Instruments or Handling Conditions. All
experiments were performed in triplicates. MCF-7
cells (1 million per sample) were subjected to
ChIP assay with anti-RNA Polymerase II (Pol 2)
antibody followed by qPCR analysis of the
proximal promoter of GAPDH, and an ORF-free
region (IGX1A). Researcher A & B performed
the PCR assays either in a 96-well plate or
384-well plate format on a Stratagene MX 3005 or
an ABI 7900 Real-Time PCR instrument
respectively, using the same ChIP DNA sample
stored as indicated. The results demonstrate
high reproducibility of PCR performance.

Sensitivity
Together with the straightforward One-Day ChIP kit and ChIP-Grade Antibody Kits, 100% effective call rates are obtained with ChIP DNA from as little as one million cells per assay.

Ct Range

Percent Distribution of Ct
Values

Input

H3K4me3

Control IgG

<24

0%

27%

0%

25-30

100%

60%

0%

30-35

0%

13%

96%

Absent Calls

0%

0%

4%

Table 1. ChIP PCR Arrays Analyze the Enrichment of 84 Genomic Sites with
as Little as One Million Cells. P19 mouse
embryonic carcinoma cells were prepared for the
EpiTect ChIP PCR Array using the EpiTect ChIP
One-Day Kit and anti-H3K4me3 Antibody Kit. One
million cells were used as starting material for
each ChIP Array (ChIP fraction). The purified
ChIP DNA samples were characterized using Mouse
Stem Cell Transcription Factor ChIP PCR Array
with 1/100th of the ChIP DNA as template in each
well. The Real-Time PCR results demonstrate 100
% effective call rates for the Input Fraction
(Ct < 30). The difference of Ct value between
the anti-H3K4me3 antibody and the control IgG
fractions indicates the specific enrichment of
the antibody, whereas the high Ct value of the
control IgG fraction indicates the low
background of the assay.